diff --git a/Utilities.md b/Utilities.md index 1c8d83d..9d73c27 100644 --- a/Utilities.md +++ b/Utilities.md @@ -10,30 +10,30 @@ All utilities are written in Python and contain headers that provide information | Category | [Script name](https://github.com/Katzlab/PhyloToL-6/tree/main/Utilities) | Intent | Output | | ----------------------------- | ------------------------------------------------------------------------ | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------------- | -| Assembly and fasta tools | Assess_transcriptomes_v2.0.py | Calculates the length, GC content, and coverage of assembled files | Spreadsheet containing the length, coverage, and GC of each transcript. | -| | Cluster_v2.0.py | Clusters sequences in a fasta file | Clustered fasta files | -| | GetTaxonomy_v1.0.py | Collects taxonomic classification of organisms from NCBI | Spreadsheet with NCBI taxonomy | -| | GetUniqueTaxa_v1.0.py | Gets the unique taxa from a taxonomic classification | Spreadsheet with unique taxa | -| | Plot_transcriptomes_v2.0.py | Plots the length, coverage, and GC distribution of transcriptomes. | Plots of transcripts distribution. | -| | QuerySRA_v1.0.py | Downloads assemblies from NCBI | Assemblies, IDs, and GCA or SRR codes. | -| | ReadMapping_v2.0.py | Maps a group of trimmed reads to a reference | Sam/Bam files. | -| | SeqLenToCsv_v1.0.py | Calculates the length of DNA sequences in fasta files | Spreadsheet containing the length of all sequences. | -| | SharedOGs_v1.0.py | Summarizes the gene family presence in fasta files | Spreadsheet with the gene families | +| Assembly and fasta tools | Assess_transcriptomes.py | Calculates the length, GC content, and coverage of assembled files | Spreadsheet containing the length, coverage, and GC of each transcript. | +| | Cluster.py | Clusters sequences in a fasta file | Clustered fasta files | +| | GetTaxonomy.py | Collects taxonomic classification of organisms from NCBI | Spreadsheet with NCBI taxonomy | +| | GetUniqueTaxa.py | Gets the unique taxa from a taxonomic classification | Spreadsheet with unique taxa | +| | Plot_transcriptomes.py | Plots the length, coverage, and GC distribution of transcriptomes. | Plots of transcripts distribution. | +| | QuerySRA.py | Downloads assemblies from NCBI | Assemblies, IDs, and GCA or SRR codes. | +| | ReadMapping.py | Maps a group of trimmed reads to a reference | Sam/Bam files. | +| | SeqLenToCsv.py | Calculates the length of DNA sequences in fasta files | Spreadsheet containing the length of all sequences. | +| | SharedOGs.py | Summarizes the gene family presence in fasta files | Spreadsheet with the gene families | | | | | | -| Sequence composition analysis | CUB_v2.1.py | Summarizes the nucleotide composition of fasta files | Fasta file and several spreadsheets summarizing the nucelotide composition | -| | GC_identifier_v1.0.py | Renames sequence ID by GC composition | Fasta files with relabeled sequence ID | -| | PlotComps_v2.0.r | Produces GC3 width plots | GC3 width plots | -| | Plotcomps_SppName_v1.0.R | Produces GC3 width plots with the species name and # seqs added to each plot | GC3 width plots | +| Sequence composition analysis | CUB.py | Summarizes the nucleotide composition of fasta files | Fasta file and several spreadsheets summarizing the nucelotide composition | +| | GC_identifier.py | Renames sequence ID by GC composition | Fasta files with relabeled sequence ID | +| | PlotComps.r | Produces GC3 width plots | GC3 width plots | +| | Plotcomps_SppName.R | Produces GC3 width plots with the species name and # seqs added to each plot | GC3 width plots | | | | | | | MSA tools | BacktranslateAlignment.py | Produces new nucleotide alignment from an amino acid alignment | Aligned nucelotide file | -| | CountTaxonOccurence_v2.0.py | Counts the occurences of each taxa in each gene family of a post guidance file | Spreadsheet with counts of taxa | -| | friendlessness_v2.0.py | Describes the internal regions of insertion unique or nearly unique to a sequence | Spreadsheet with each sequence statistics | -| | Gappiness_v2.0.py | Produces statistics on the terminal and internal gaps of an alignment | Spreadsheet with the paralogs statistics | -| | GuidanceWrapper_v2.1.py | Guidance wrapper that can be used in place of PhyloToL pipeline | Guidanced alignment files | +| | CountTaxonOccurence.py | Counts the occurences of each taxa in each gene family of a post guidance file | Spreadsheet with counts of taxa | +| | friendlessness.py | Describes the internal regions of insertion unique or nearly unique to a sequence | Spreadsheet with each sequence statistics | +| | Gappiness.py | Produces statistics on the terminal and internal gaps of an alignment | Spreadsheet with the paralogs statistics | +| | GuidanceWrapper.py | Guidance wrapper that can be used in place of PhyloToL pipeline | Guidanced alignment files | | | | | | -| Gene tree description | CladeSizes_v2.0.py | Describes clade sizes for different taxonomic groups | Spreadsheet describing clade sizes | -| | ColorByClade_v2.1.py | Visualizes placement of taxa by taxonomic group in trees | Colored trees | -| | ContaminationBySisters_v2.2.py | Summarizes the taxonomic distribution of sister sequences for each taxon in a tree | Two spreadsheets summarizing tree tips relationship | -| | RenameTips_v1.0.py | Renames the tip labels of trees to include metadata such as location and date | Renamed trees | +| Gene tree description | CladeSizes.py | Describes clade sizes for different taxonomic groups | Spreadsheet describing clade sizes | +| | ColorByClade.py | Visualizes placement of taxa by taxonomic group in trees | Colored trees | +| | ContaminationBySisters.py | Summarizes the taxonomic distribution of sister sequences for each taxon in a tree | Two spreadsheets summarizing tree tips relationship | +| | RenameTips.py | Renames the tip labels of trees to include metadata such as location and date | Renamed trees | | | | | | -| Stand-alone clade grabbing | CladeGrabbing_v2.1.py | Selects clades of interest from trees using taxonomic specifications | Phylogenetic trees | \ No newline at end of file +| Stand-alone clade grabbing | CladeGrabbing.py | Selects clades of interest from trees using taxonomic specifications | Phylogenetic trees | \ No newline at end of file